view variant_effect_predictor/Bio/EnsEMBL/Mapper/Coordinate.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

Bio::EnsEMBL::Mapper::Coordinate

=head1 SYNOPSIS

=head1 DESCRIPTION

Representation of a mapped region in a sequence; returned from Mapper.pm
when the target region maps on to valid sequence.

=head1 METHODS

=cut

package Bio::EnsEMBL::Mapper::Coordinate;

use strict;

=head2 new

  Arg [1]     char|int id of object in mapped region
  Arg [2]     int start of region   
  Arg [3]     int end of region
  Arg [4]     int strand if region
  Arg [5]     Bio::EnsEMBL::CoordSystem  coordsytem of the region
  Function    creates a new Coordinate object
  Returntype  Bio::EnsEMBL::Mapper::Coordinate
  Exceptions  none
  Status      Stable

=cut

sub new {
  my ( $proto, $id, $start, $end, $strand, $coord_system, $rank ) = @_;

  my $class = ref($proto) || $proto;

  return
    bless( { 'id'           => $id,
             'start'        => $start,
             'end'          => $end,
             'strand'       => $strand,
             'coord_system' => $coord_system,
             'rank'         => $rank || 0
           },
           $class );
}


=head2 start

  Arg  1      int $start
              start coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

=cut

sub start {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'start'} = $value;
  }

  return $self->{'start'};
}


=head2 end

  Arg  1      int $end
              end coordinate of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

=cut

sub end {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'end'} = $value;
  }

  return $self->{'end'};
}

=head2 strand

  Arg  1      int $strand
              strand of object in mapped region
  Function    getter/setter method
  Returntype  int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

=cut

sub strand {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'strand'} = $value;
  }

  return $self->{'strand'};
}

=head2 id

  Arg  1      char|int $id
              id of object in mapped region
	      e.g. seq_region_id / seq_region_name
  Function    getter/setter method
  Returntype  char|int
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

=cut

sub id {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'id'} = $value;
  }

  return $self->{'id'};
}

=head2 coord_system

  Arg  1      Bio::EnsEMBL::CoordSystem
  Function    getter/setter method
  Returntype  Bio::EnsEMBL::CoordSystem
  Exceptions  none
  Caller      Bio::EnsEMBL::Mapper::Coordinate
  Status      Stable

=cut

sub coord_system {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'coord_system'} = $value;
  }

  return $self->{'coord_system'};
}

=head2 length

  Function    getter method
  Returntype  int
  Exceptions  none
  Caller      ?
  Status      Stable

=cut

sub length {
  my ($self) = @_;

  return $self->{'end'} - $self->{'start'} + 1;
}

sub rank {
  my ( $self, $value ) = @_;

  if ( defined($value) ) {
    $self->{'rank'} = $value;
  }

  return $self->{'rank'};
}

1;